Identification of differentially expressed UniGenes in developing wheat seed using Digital Differential Display

Abstract

The wheat UniGene sets, derived from over one million Expressed Sequence Tags (ESTs) in the NCBI GenBank, offer a platform for identifying differentially expressed genes in wheat seeds. This report illustrates a means to efficiently utilize this public database for gene expression (transcriptome) profiling of developing wheat seed. Using a data mining tool known as Digital Differential Display (DDD), thirteen pair-wise comparisons were performed on seven seed cDNA libraries from five varieties at various seed development stages. DDD identified 46 seed-specific UniGene sets, excluding the well characterized “housekeeping” and seed storage protein genes. Additionally, seed- and developmentally-specific UniGenes were identified. Some of these genes encode for proteins such as purothionins, serpins, α-amylase inhibitors, lipid transfer proteins, and other unknown but novel gene sequences. Specifically, the wheat serpin and β-purothionin precursor were found to be expressed at higher levels in hard varieties than soft varieties. This study supports the starting premise that by implementing in-silico analysis of the wheat UniGene database, it is possible to rapidly create transcriptional profiles of known and novel genes in developing seeds.